should i delete these empty keyframes?
To extend Delagone's comment: It does not matter.

But every time you delete these keys (autokey), you're doing unnecessary work. Time which you could spend setting new key, which you need. I advise you to get used to having lots of keys around.

Another pitfall is to accidentally change the transformations later, if you have channels, which aren't keyed, you're going to loose the values you had before. Leave your additional keys in place, even if they don't seem necessary. Quite a lot animators even key all channels regardless how small the amount of channels (bones, etc) is that they changed, just so a characters pose if fixed, no matter what attributes / channels are changed later.

If the additional keys still disturb you, here is a workaround.
After moving your bones / objects to their initial transform, lock all attributes, which you don't want to key. Then create a button keying set with the channels you want to animate. Then set the active keying set, to the one you created. If you're using autokey, check the keying set button next to the autokey button.